A group of Lamiaceae that has caused confusion over its generic boundaries are those species belonging to the complex surrounding the genera Satureja, Calamintha, Micromeria, Clinopodium and Acinos. In the current study, cross sections of root and stem of six Clinopodium taxa, previously treated as Acinos in Flora of Turkey, is studied for the first time and detailed descriptions and illustrations of root and stem are described and illustrated here. It is taxonomically interesting that the root and stems of these 6 taxa show similar histological characters except for a few differences, such as primary tissue structure in middle part of roots of C. troodi subsp. grandiflorum, cell numbers, types and density of trichome and prominent projecting at the corners in stem cross-section. The root center of studied Clinopodium taxa has a narrow pith consisting of primery xylem cells and the pith rays are 1-2-layered. Vascular bundles in all taxa are well-developed in the corners of the stems.